heatmapsarifa
Christian Heyer
2022-05-31
## New names:
## Rows: 415 Columns: 4
## ── Column specification
## ──────────────────────────────────────────────────────── Delimiter: "\t" chr
## (1): ID dbl (3): Stromal_score, Immune_score, ESTIMATE_score
## ℹ Use `spec()` to retrieve the full column specification for this data. ℹ
## Specify the column types or set `show_col_types = FALSE` to quiet this message.
## • `SARIFA` -> `SARIFA...3`
## • `SARIFA` -> `SARIFA...4`Heatmaps
You can also embed plots, for example:
## [1] "Row names"
## [2] "ID"
## [3] "Stromal score"
## [4] "Immune score"
## [5] "ESTIMATE score"
## [6] "Row names y"
## [7] "sarifa group"
## [8] "barcode"
## [9] "patient"
## [10] "sample"
## [11] "shortLetterCode"
## [12] "definition"
## [13] "sample submitter id"
## [14] "sample type id"
## [15] "tumor descriptor"
## [16] "sample id"
## [17] "sample type"
## [18] "composition"
## [19] "days to collection"
## [20] "state"
## [21] "initial weight"
## [22] "intermediate dimension"
## [23] "pathology report uuid"
## [24] "submitter id"
## [25] "shortest dimension"
## [26] "oct embedded"
## [27] "longest dimension"
## [28] "is ffpe"
## [29] "tissue type"
## [30] "synchronous malignancy"
## [31] "ajcc pathologic stage"
## [32] "days to diagnosis"
## [33] "treatments"
## [34] "last known disease status"
## [35] "tissue or organ of origin"
## [36] "days to last follow up"
## [37] "age at diagnosis"
## [38] "primary diagnosis"
## [39] "prior malignancy"
## [40] "year of diagnosis"
## [41] "prior treatment"
## [42] "ajcc staging system edition"
## [43] "ajcc pathologic t"
## [44] "morphology"
## [45] "ajcc pathologic n"
## [46] "ajcc pathologic m"
## [47] "classification of tumor"
## [48] "diagnosis id"
## [49] "icd 10 code"
## [50] "site of resection or biopsy"
## [51] "tumor grade"
## [52] "progression or recurrence"
## [53] "alcohol history"
## [54] "exposure id"
## [55] "race"
## [56] "gender"
## [57] "ethnicity"
## [58] "vital status"
## [59] "age at index"
## [60] "days to birth"
## [61] "year of birth"
## [62] "demographic id"
## [63] "year of death"
## [64] "days to death"
## [65] "bcr patient barcode"
## [66] "primary site"
## [67] "project id"
## [68] "disease type"
## [69] "name"
## [70] "releasable"
## [71] "released"
## [72] "patient"
## [73] "Lauren Class"
## [74] "Intestinal Type Subclass"
## [75] "Signet Ring"
## [76] "WHO Class"
## [77] "Pathologic T"
## [78] "Pathologic N"
## [79] "Pathologic M"
## [80] "TNM Stage"
## [81] "Anatomic Region"
## [82] "Residual Tumor"
## [83] "Age at Initial Diagnosis"
## [84] "Country"
## [85] "Gender"
## [86] "Race"
## [87] "Vital Status"
## [88] "Days to Last Follow up"
## [89] "Days to Death"
## [90] "Recurrence"
## [91] "Days to Recurrence"
## [92] "Molecular Subtype"
## [93] "Total Mutation Rate"
## [94] "Hypermutated"
## [95] "MLH1 Epigenetically Silenced"
## [96] "CDKN2A Epigenetically Silenced"
## [97] "MSI status"
## [98] "EBV positive"
## [99] "TP53 mutation"
## [100] "PIK3CA mutation"
## [101] "KRAS mutation"
## [102] "ARID1A mutation"
## [103] "RHOA mutation"
## [104] "ARHGAP26 ARHGAP6 CLDN18 Rearrangement"
## [105] "MET Skipped Exon 2"
## [106] "MET Skipped Exons 18 and 19"
## [107] "ABSOLUTE Ploidy"
## [108] "ABSOLUTE Purity"
## [109] "Estimated Leukocyte Percentage"
## [110] "Percent Tumor Nuclei"
## [111] "Percent Tumor Cells"
## [112] "Percent Lymphocyte Infiltration"
## [113] "Gene Expression Cluster"
## [114] "MicroRNA Expression Cluster"
## [115] "Copy Number Cluster"
## [116] "Methylation Cluster"
## [117] "CIMP Category"
## [118] "stringAsFactor"
## [119] "sizeFactor"
## [120] "replaceable"
## [121] "Study ID"
## [122] "Kommentar"
## [123] "SARIFA 3"
## [124] "SARIFA 4"
## [125] "SARIFAreduziert"
## [126] "Sample ID"
## [127] "Diagnosis Age"
## [128] "Neoplasm Disease Stage American Joint Committee on Cancer Code"
## [129] "American Joint Committee on Cancer Publication Version Type"
## [130] "Aneuploidy Score"
## [131] "Cancer Type"
## [132] "TCGA PanCanAtlas Cancer Type Acronym"
## [133] "Cancer Type Detailed"
## [134] "Center of sequencing"
## [135] "Last Communication Contact from Initial Pathologic Diagnosis Date"
## [136] "Birth from Initial Pathologic Diagnosis Date"
## [137] "Last Alive Less Initial Pathologic Diagnosis Date Calculated Day Value"
## [138] "Disease Free (Months)"
## [139] "Disease Free Status"
## [140] "Months of disease-specific survival"
## [141] "Disease-specific Survival status"
## [142] "Ethnicity Category"
## [143] "Form completion date"
## [144] "Fraction Genome Altered"
## [145] "Neoplasm Histologic Grade"
## [146] "Neoadjuvant Therapy Type Administered Prior To Resection Text"
## [147] "ICD-10 Classification"
## [148] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code"
## [149] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code"
## [150] "Informed consent verified"
## [151] "In PanCan Pathway Analysis"
## [152] "MSI MANTIS Score"
## [153] "MSIsensor Score"
## [154] "Mutation Count"
## [155] "New Neoplasm Event Post Initial Therapy Indicator"
## [156] "Oncotree Code"
## [157] "Overall Survival (Months)"
## [158] "Overall Survival Status"
## [159] "Other Patient ID"
## [160] "American Joint Committee on Cancer Metastasis Stage Code"
## [161] "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code"
## [162] "American Joint Committee on Cancer Tumor Stage Code"
## [163] "Person Neoplasm Cancer Status"
## [164] "Progress Free Survival (Months)"
## [165] "Progression Free Status"
## [166] "Primary Lymph Node Presentation Assessment"
## [167] "Prior Diagnosis"
## [168] "Race Category"
## [169] "Radiation Therapy"
## [170] "Number of Samples Per Patient"
## [171] "Sample Type"
## [172] "Sex"
## [173] "Somatic Status"
## [174] "Subtype"
## [175] "Tissue Prospective Collection Indicator"
## [176] "Tissue Retrospective Collection Indicator"
## [177] "Tissue Source Site"
## [178] "TMB (nonsynonymous)"
## [179] "Tumor Disease Anatomic Site"
## [180] "Tumor Type"
## [181] "Patient Weight"
## [1] "Row names"
## [2] "ID"
## [3] "Stromal score"
## [4] "Immune score"
## [5] "ESTIMATE score"
## [6] "Row names y"
## [7] "sarifa group"
## [8] "barcode"
## [9] "patient"
## [10] "sample"
## [11] "shortLetterCode"
## [12] "definition"
## [13] "sample submitter id"
## [14] "sample type id"
## [15] "tumor descriptor"
## [16] "sample id"
## [17] "sample type"
## [18] "composition"
## [19] "days to collection"
## [20] "state"
## [21] "initial weight"
## [22] "intermediate dimension"
## [23] "pathology report uuid"
## [24] "submitter id"
## [25] "shortest dimension"
## [26] "oct embedded"
## [27] "longest dimension"
## [28] "is ffpe"
## [29] "tissue type"
## [30] "synchronous malignancy"
## [31] "ajcc pathologic stage"
## [32] "days to diagnosis"
## [33] "treatments"
## [34] "last known disease status"
## [35] "tissue or organ of origin"
## [36] "days to last follow up"
## [37] "age at diagnosis"
## [38] "primary diagnosis"
## [39] "prior malignancy"
## [40] "year of diagnosis"
## [41] "prior treatment"
## [42] "ajcc staging system edition"
## [43] "ajcc pathologic t"
## [44] "morphology"
## [45] "ajcc pathologic n"
## [46] "ajcc pathologic m"
## [47] "classification of tumor"
## [48] "diagnosis id"
## [49] "icd 10 code"
## [50] "site of resection or biopsy"
## [51] "tumor grade"
## [52] "progression or recurrence"
## [53] "alcohol history"
## [54] "exposure id"
## [55] "race"
## [56] "gender"
## [57] "ethnicity"
## [58] "vital status"
## [59] "age at index"
## [60] "days to birth"
## [61] "year of birth"
## [62] "demographic id"
## [63] "year of death"
## [64] "days to death"
## [65] "bcr patient barcode"
## [66] "primary site"
## [67] "project id"
## [68] "disease type"
## [69] "name"
## [70] "releasable"
## [71] "released"
## [72] "patient"
## [73] "Lauren Class"
## [74] "Intestinal Type Subclass"
## [75] "Signet Ring"
## [76] "WHO Class"
## [77] "Pathologic T"
## [78] "Pathologic N"
## [79] "Pathologic M"
## [80] "TNM Stage"
## [81] "Anatomic Region"
## [82] "Residual Tumor"
## [83] "Age at Initial Diagnosis"
## [84] "Country"
## [85] "Gender"
## [86] "Race"
## [87] "Vital Status"
## [88] "Days to Last Follow up"
## [89] "Days to Death"
## [90] "Recurrence"
## [91] "Days to Recurrence"
## [92] "Molecular Subtype"
## [93] "Total Mutation Rate"
## [94] "Hypermutated"
## [95] "MLH1 Epigenetically Silenced"
## [96] "CDKN2A Epigenetically Silenced"
## [97] "MSI status"
## [98] "EBV positive"
## [99] "TP53 mutation"
## [100] "PIK3CA mutation"
## [101] "KRAS mutation"
## [102] "ARID1A mutation"
## [103] "RHOA mutation"
## [104] "ARHGAP26 ARHGAP6 CLDN18 Rearrangement"
## [105] "MET Skipped Exon 2"
## [106] "MET Skipped Exons 18 and 19"
## [107] "ABSOLUTE Ploidy"
## [108] "ABSOLUTE Purity"
## [109] "Estimated Leukocyte Percentage"
## [110] "Percent Tumor Nuclei"
## [111] "Percent Tumor Cells"
## [112] "Percent Lymphocyte Infiltration"
## [113] "Gene Expression Cluster"
## [114] "MicroRNA Expression Cluster"
## [115] "Copy Number Cluster"
## [116] "Methylation Cluster"
## [117] "CIMP Category"
## [118] "stringAsFactor"
## [119] "sizeFactor"
## [120] "replaceable"
## [121] "Study ID"
## [122] "Kommentar"
## [123] "SARIFA 3"
## [124] "SARIFA 4"
## [125] "SARIFAreduziert"
## [126] "Sample ID"
## [127] "Diagnosis Age"
## [128] "Neoplasm Disease Stage American Joint Committee on Cancer Code"
## [129] "American Joint Committee on Cancer Publication Version Type"
## [130] "Aneuploidy Score"
## [131] "Cancer Type"
## [132] "TCGA PanCanAtlas Cancer Type Acronym"
## [133] "Cancer Type Detailed"
## [134] "Center of sequencing"
## [135] "Last Communication Contact from Initial Pathologic Diagnosis Date"
## [136] "Birth from Initial Pathologic Diagnosis Date"
## [137] "Last Alive Less Initial Pathologic Diagnosis Date Calculated Day Value"
## [138] "Disease Free (Months)"
## [139] "Disease Free Status"
## [140] "Months of disease-specific survival"
## [141] "Disease-specific Survival status"
## [142] "Ethnicity Category"
## [143] "Form completion date"
## [144] "Fraction Genome Altered"
## [145] "Neoplasm Histologic Grade"
## [146] "Neoadjuvant Therapy Type Administered Prior To Resection Text"
## [147] "ICD-10 Classification"
## [148] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code"
## [149] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code"
## [150] "Informed consent verified"
## [151] "In PanCan Pathway Analysis"
## [152] "MSI MANTIS Score"
## [153] "MSIsensor Score"
## [154] "Mutation Count"
## [155] "New Neoplasm Event Post Initial Therapy Indicator"
## [156] "Oncotree Code"
## [157] "Overall Survival (Months)"
## [158] "Overall Survival Status"
## [159] "Other Patient ID"
## [160] "American Joint Committee on Cancer Metastasis Stage Code"
## [161] "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code"
## [162] "American Joint Committee on Cancer Tumor Stage Code"
## [163] "Person Neoplasm Cancer Status"
## [164] "Progress Free Survival (Months)"
## [165] "Progression Free Status"
## [166] "Primary Lymph Node Presentation Assessment"
## [167] "Prior Diagnosis"
## [168] "Race Category"
## [169] "Radiation Therapy"
## [170] "Number of Samples Per Patient"
## [171] "Sample Type"
## [172] "Sex"
## [173] "Somatic Status"
## [174] "Subtype"
## [175] "Tissue Prospective Collection Indicator"
## [176] "Tissue Retrospective Collection Indicator"
## [177] "Tissue Source Site"
## [178] "TMB (nonsynonymous)"
## [179] "Tumor Disease Anatomic Site"
## [180] "Tumor Type"
## [181] "Patient Weight"
Strict
## [1] "Row names"
## [2] "ID"
## [3] "Stromal score"
## [4] "Immune score"
## [5] "ESTIMATE score"
## [6] "Row names y"
## [7] "sarifa group"
## [8] "barcode"
## [9] "patient"
## [10] "sample"
## [11] "shortLetterCode"
## [12] "definition"
## [13] "sample submitter id"
## [14] "sample type id"
## [15] "tumor descriptor"
## [16] "sample id"
## [17] "sample type"
## [18] "composition"
## [19] "days to collection"
## [20] "state"
## [21] "initial weight"
## [22] "intermediate dimension"
## [23] "pathology report uuid"
## [24] "submitter id"
## [25] "shortest dimension"
## [26] "oct embedded"
## [27] "longest dimension"
## [28] "is ffpe"
## [29] "tissue type"
## [30] "synchronous malignancy"
## [31] "ajcc pathologic stage"
## [32] "days to diagnosis"
## [33] "treatments"
## [34] "last known disease status"
## [35] "tissue or organ of origin"
## [36] "days to last follow up"
## [37] "age at diagnosis"
## [38] "primary diagnosis"
## [39] "prior malignancy"
## [40] "year of diagnosis"
## [41] "prior treatment"
## [42] "ajcc staging system edition"
## [43] "ajcc pathologic t"
## [44] "morphology"
## [45] "ajcc pathologic n"
## [46] "ajcc pathologic m"
## [47] "classification of tumor"
## [48] "diagnosis id"
## [49] "icd 10 code"
## [50] "site of resection or biopsy"
## [51] "tumor grade"
## [52] "progression or recurrence"
## [53] "alcohol history"
## [54] "exposure id"
## [55] "race"
## [56] "gender"
## [57] "ethnicity"
## [58] "vital status"
## [59] "age at index"
## [60] "days to birth"
## [61] "year of birth"
## [62] "demographic id"
## [63] "year of death"
## [64] "days to death"
## [65] "bcr patient barcode"
## [66] "primary site"
## [67] "project id"
## [68] "disease type"
## [69] "name"
## [70] "releasable"
## [71] "released"
## [72] "patient"
## [73] "Lauren Class"
## [74] "Intestinal Type Subclass"
## [75] "Signet Ring"
## [76] "WHO Class"
## [77] "Pathologic T"
## [78] "Pathologic N"
## [79] "Pathologic M"
## [80] "TNM Stage"
## [81] "Anatomic Region"
## [82] "Residual Tumor"
## [83] "Age at Initial Diagnosis"
## [84] "Country"
## [85] "Gender"
## [86] "Race"
## [87] "Vital Status"
## [88] "Days to Last Follow up"
## [89] "Days to Death"
## [90] "Recurrence"
## [91] "Days to Recurrence"
## [92] "Molecular Subtype"
## [93] "Total Mutation Rate"
## [94] "Hypermutated"
## [95] "MLH1 Epigenetically Silenced"
## [96] "CDKN2A Epigenetically Silenced"
## [97] "MSI status"
## [98] "EBV positive"
## [99] "TP53 mutation"
## [100] "PIK3CA mutation"
## [101] "KRAS mutation"
## [102] "ARID1A mutation"
## [103] "RHOA mutation"
## [104] "ARHGAP26 ARHGAP6 CLDN18 Rearrangement"
## [105] "MET Skipped Exon 2"
## [106] "MET Skipped Exons 18 and 19"
## [107] "ABSOLUTE Ploidy"
## [108] "ABSOLUTE Purity"
## [109] "Estimated Leukocyte Percentage"
## [110] "Percent Tumor Nuclei"
## [111] "Percent Tumor Cells"
## [112] "Percent Lymphocyte Infiltration"
## [113] "Gene Expression Cluster"
## [114] "MicroRNA Expression Cluster"
## [115] "Copy Number Cluster"
## [116] "Methylation Cluster"
## [117] "CIMP Category"
## [118] "stringAsFactor"
## [119] "sizeFactor"
## [120] "replaceable"
## [121] "Study ID"
## [122] "Kommentar"
## [123] "SARIFA 3"
## [124] "SARIFA 4"
## [125] "SARIFAreduziert"
## [126] "Sample ID"
## [127] "Diagnosis Age"
## [128] "Neoplasm Disease Stage American Joint Committee on Cancer Code"
## [129] "American Joint Committee on Cancer Publication Version Type"
## [130] "Aneuploidy Score"
## [131] "Cancer Type"
## [132] "TCGA PanCanAtlas Cancer Type Acronym"
## [133] "Cancer Type Detailed"
## [134] "Center of sequencing"
## [135] "Last Communication Contact from Initial Pathologic Diagnosis Date"
## [136] "Birth from Initial Pathologic Diagnosis Date"
## [137] "Last Alive Less Initial Pathologic Diagnosis Date Calculated Day Value"
## [138] "Disease Free (Months)"
## [139] "Disease Free Status"
## [140] "Months of disease-specific survival"
## [141] "Disease-specific Survival status"
## [142] "Ethnicity Category"
## [143] "Form completion date"
## [144] "Fraction Genome Altered"
## [145] "Neoplasm Histologic Grade"
## [146] "Neoadjuvant Therapy Type Administered Prior To Resection Text"
## [147] "ICD-10 Classification"
## [148] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code"
## [149] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code"
## [150] "Informed consent verified"
## [151] "In PanCan Pathway Analysis"
## [152] "MSI MANTIS Score"
## [153] "MSIsensor Score"
## [154] "Mutation Count"
## [155] "New Neoplasm Event Post Initial Therapy Indicator"
## [156] "Oncotree Code"
## [157] "Overall Survival (Months)"
## [158] "Overall Survival Status"
## [159] "Other Patient ID"
## [160] "American Joint Committee on Cancer Metastasis Stage Code"
## [161] "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code"
## [162] "American Joint Committee on Cancer Tumor Stage Code"
## [163] "Person Neoplasm Cancer Status"
## [164] "Progress Free Survival (Months)"
## [165] "Progression Free Status"
## [166] "Primary Lymph Node Presentation Assessment"
## [167] "Prior Diagnosis"
## [168] "Race Category"
## [169] "Radiation Therapy"
## [170] "Number of Samples Per Patient"
## [171] "Sample Type"
## [172] "Sex"
## [173] "Somatic Status"
## [174] "Subtype"
## [175] "Tissue Prospective Collection Indicator"
## [176] "Tissue Retrospective Collection Indicator"
## [177] "Tissue Source Site"
## [178] "TMB (nonsynonymous)"
## [179] "Tumor Disease Anatomic Site"
## [180] "Tumor Type"
## [181] "Patient Weight"
## [1] "Row names"
## [2] "ID"
## [3] "Stromal score"
## [4] "Immune score"
## [5] "ESTIMATE score"
## [6] "Row names y"
## [7] "sarifa group"
## [8] "barcode"
## [9] "patient"
## [10] "sample"
## [11] "shortLetterCode"
## [12] "definition"
## [13] "sample submitter id"
## [14] "sample type id"
## [15] "tumor descriptor"
## [16] "sample id"
## [17] "sample type"
## [18] "composition"
## [19] "days to collection"
## [20] "state"
## [21] "initial weight"
## [22] "intermediate dimension"
## [23] "pathology report uuid"
## [24] "submitter id"
## [25] "shortest dimension"
## [26] "oct embedded"
## [27] "longest dimension"
## [28] "is ffpe"
## [29] "tissue type"
## [30] "synchronous malignancy"
## [31] "ajcc pathologic stage"
## [32] "days to diagnosis"
## [33] "treatments"
## [34] "last known disease status"
## [35] "tissue or organ of origin"
## [36] "days to last follow up"
## [37] "age at diagnosis"
## [38] "primary diagnosis"
## [39] "prior malignancy"
## [40] "year of diagnosis"
## [41] "prior treatment"
## [42] "ajcc staging system edition"
## [43] "ajcc pathologic t"
## [44] "morphology"
## [45] "ajcc pathologic n"
## [46] "ajcc pathologic m"
## [47] "classification of tumor"
## [48] "diagnosis id"
## [49] "icd 10 code"
## [50] "site of resection or biopsy"
## [51] "tumor grade"
## [52] "progression or recurrence"
## [53] "alcohol history"
## [54] "exposure id"
## [55] "race"
## [56] "gender"
## [57] "ethnicity"
## [58] "vital status"
## [59] "age at index"
## [60] "days to birth"
## [61] "year of birth"
## [62] "demographic id"
## [63] "year of death"
## [64] "days to death"
## [65] "bcr patient barcode"
## [66] "primary site"
## [67] "project id"
## [68] "disease type"
## [69] "name"
## [70] "releasable"
## [71] "released"
## [72] "patient"
## [73] "Lauren Class"
## [74] "Intestinal Type Subclass"
## [75] "Signet Ring"
## [76] "WHO Class"
## [77] "Pathologic T"
## [78] "Pathologic N"
## [79] "Pathologic M"
## [80] "TNM Stage"
## [81] "Anatomic Region"
## [82] "Residual Tumor"
## [83] "Age at Initial Diagnosis"
## [84] "Country"
## [85] "Gender"
## [86] "Race"
## [87] "Vital Status"
## [88] "Days to Last Follow up"
## [89] "Days to Death"
## [90] "Recurrence"
## [91] "Days to Recurrence"
## [92] "Molecular Subtype"
## [93] "Total Mutation Rate"
## [94] "Hypermutated"
## [95] "MLH1 Epigenetically Silenced"
## [96] "CDKN2A Epigenetically Silenced"
## [97] "MSI status"
## [98] "EBV positive"
## [99] "TP53 mutation"
## [100] "PIK3CA mutation"
## [101] "KRAS mutation"
## [102] "ARID1A mutation"
## [103] "RHOA mutation"
## [104] "ARHGAP26 ARHGAP6 CLDN18 Rearrangement"
## [105] "MET Skipped Exon 2"
## [106] "MET Skipped Exons 18 and 19"
## [107] "ABSOLUTE Ploidy"
## [108] "ABSOLUTE Purity"
## [109] "Estimated Leukocyte Percentage"
## [110] "Percent Tumor Nuclei"
## [111] "Percent Tumor Cells"
## [112] "Percent Lymphocyte Infiltration"
## [113] "Gene Expression Cluster"
## [114] "MicroRNA Expression Cluster"
## [115] "Copy Number Cluster"
## [116] "Methylation Cluster"
## [117] "CIMP Category"
## [118] "stringAsFactor"
## [119] "sizeFactor"
## [120] "replaceable"
## [121] "Study ID"
## [122] "Kommentar"
## [123] "SARIFA 3"
## [124] "SARIFA 4"
## [125] "SARIFAreduziert"
## [126] "Sample ID"
## [127] "Diagnosis Age"
## [128] "Neoplasm Disease Stage American Joint Committee on Cancer Code"
## [129] "American Joint Committee on Cancer Publication Version Type"
## [130] "Aneuploidy Score"
## [131] "Cancer Type"
## [132] "TCGA PanCanAtlas Cancer Type Acronym"
## [133] "Cancer Type Detailed"
## [134] "Center of sequencing"
## [135] "Last Communication Contact from Initial Pathologic Diagnosis Date"
## [136] "Birth from Initial Pathologic Diagnosis Date"
## [137] "Last Alive Less Initial Pathologic Diagnosis Date Calculated Day Value"
## [138] "Disease Free (Months)"
## [139] "Disease Free Status"
## [140] "Months of disease-specific survival"
## [141] "Disease-specific Survival status"
## [142] "Ethnicity Category"
## [143] "Form completion date"
## [144] "Fraction Genome Altered"
## [145] "Neoplasm Histologic Grade"
## [146] "Neoadjuvant Therapy Type Administered Prior To Resection Text"
## [147] "ICD-10 Classification"
## [148] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code"
## [149] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code"
## [150] "Informed consent verified"
## [151] "In PanCan Pathway Analysis"
## [152] "MSI MANTIS Score"
## [153] "MSIsensor Score"
## [154] "Mutation Count"
## [155] "New Neoplasm Event Post Initial Therapy Indicator"
## [156] "Oncotree Code"
## [157] "Overall Survival (Months)"
## [158] "Overall Survival Status"
## [159] "Other Patient ID"
## [160] "American Joint Committee on Cancer Metastasis Stage Code"
## [161] "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code"
## [162] "American Joint Committee on Cancer Tumor Stage Code"
## [163] "Person Neoplasm Cancer Status"
## [164] "Progress Free Survival (Months)"
## [165] "Progression Free Status"
## [166] "Primary Lymph Node Presentation Assessment"
## [167] "Prior Diagnosis"
## [168] "Race Category"
## [169] "Radiation Therapy"
## [170] "Number of Samples Per Patient"
## [171] "Sample Type"
## [172] "Sex"
## [173] "Somatic Status"
## [174] "Subtype"
## [175] "Tissue Prospective Collection Indicator"
## [176] "Tissue Retrospective Collection Indicator"
## [177] "Tissue Source Site"
## [178] "TMB (nonsynonymous)"
## [179] "Tumor Disease Anatomic Site"
## [180] "Tumor Type"
## [181] "Patient Weight"## The automatically generated colors map from the minus and plus 99^th of
## the absolute values in the matrix. There are outliers in the matrix
## whose patterns might be hidden by this color mapping. You can manually
## set the color to `col` argument.
##
## Use `suppressMessages()` to turn off this message.
Create Column Annotation for COmplexheatmap
## `geom_smooth()` using formula = 'y ~ x'
## preparing geneSet collections...## GSEA analysis...## leading edge analysis...## done...## preparing geneSet collections...## GSEA analysis...## leading edge analysis...## done...## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
Immune cell infiltration
To check whether SARIFA is associated with processes paired with immune cell infiltration data from TIMER https://academic.oup.com/nar/article/48/W1/W509/5842187?login=true
## New names:
## Rows: 11070 Columns: 120
## ── Column specification
## ──────────────────────────────────────────────────────── Delimiter: "," chr
## (1): cell_type dbl (119): B.cell_TIMER, T.cell.CD4._TIMER, T.cell.CD8._TIMER,
## Neutrophil_TI...
## ℹ Use `spec()` to retrieve the full column specification for this data. ℹ
## Specify the column types or set `show_col_types = FALSE` to quiet this message.
## • `B cell_TIMER` -> `B.cell_TIMER`
## • `T cell CD4+_TIMER` -> `T.cell.CD4._TIMER`
## • `T cell CD8+_TIMER` -> `T.cell.CD8._TIMER`
## • `Myeloid dendritic cell_TIMER` -> `Myeloid.dendritic.cell_TIMER`
## • `B cell naive_CIBERSORT` -> `B.cell.naive_CIBERSORT`
## • `B cell memory_CIBERSORT` -> `B.cell.memory_CIBERSORT`
## • `B cell plasma_CIBERSORT` -> `B.cell.plasma_CIBERSORT`
## • `T cell CD8+_CIBERSORT` -> `T.cell.CD8._CIBERSORT`
## • `T cell CD4+ naive_CIBERSORT` -> `T.cell.CD4..naive_CIBERSORT`
## • `T cell CD4+ memory resting_CIBERSORT` ->
## `T.cell.CD4..memory.resting_CIBERSORT`
## • `T cell CD4+ memory activated_CIBERSORT` ->
## `T.cell.CD4..memory.activated_CIBERSORT`
## • `T cell follicular helper_CIBERSORT` -> `T.cell.follicular.helper_CIBERSORT`
## • `T cell regulatory (Tregs)_CIBERSORT` ->
## `T.cell.regulatory..Tregs._CIBERSORT`
## • `T cell gamma delta_CIBERSORT` -> `T.cell.gamma.delta_CIBERSORT`
## • `NK cell resting_CIBERSORT` -> `NK.cell.resting_CIBERSORT`
## • `NK cell activated_CIBERSORT` -> `NK.cell.activated_CIBERSORT`
## • `Macrophage M0_CIBERSORT` -> `Macrophage.M0_CIBERSORT`
## • `Macrophage M1_CIBERSORT` -> `Macrophage.M1_CIBERSORT`
## • `Macrophage M2_CIBERSORT` -> `Macrophage.M2_CIBERSORT`
## • `Myeloid dendritic cell resting_CIBERSORT` ->
## `Myeloid.dendritic.cell.resting_CIBERSORT`
## • `Myeloid dendritic cell activated_CIBERSORT` ->
## `Myeloid.dendritic.cell.activated_CIBERSORT`
## • `Mast cell activated_CIBERSORT` -> `Mast.cell.activated_CIBERSORT`
## • `Mast cell resting_CIBERSORT` -> `Mast.cell.resting_CIBERSORT`
## • `B cell naive_CIBERSORT-ABS` -> `B.cell.naive_CIBERSORT.ABS`
## • `B cell memory_CIBERSORT-ABS` -> `B.cell.memory_CIBERSORT.ABS`
## • `B cell plasma_CIBERSORT-ABS` -> `B.cell.plasma_CIBERSORT.ABS`
## • `T cell CD8+_CIBERSORT-ABS` -> `T.cell.CD8._CIBERSORT.ABS`
## • `T cell CD4+ naive_CIBERSORT-ABS` -> `T.cell.CD4..naive_CIBERSORT.ABS`
## • `T cell CD4+ memory resting_CIBERSORT-ABS` ->
## `T.cell.CD4..memory.resting_CIBERSORT.ABS`
## • `T cell CD4+ memory activated_CIBERSORT-ABS` ->
## `T.cell.CD4..memory.activated_CIBERSORT.ABS`
## • `T cell follicular helper_CIBERSORT-ABS` ->
## `T.cell.follicular.helper_CIBERSORT.ABS`
## • `T cell regulatory (Tregs)_CIBERSORT-ABS` ->
## `T.cell.regulatory..Tregs._CIBERSORT.ABS`
## • `T cell gamma delta_CIBERSORT-ABS` -> `T.cell.gamma.delta_CIBERSORT.ABS`
## • `NK cell resting_CIBERSORT-ABS` -> `NK.cell.resting_CIBERSORT.ABS`
## • `NK cell activated_CIBERSORT-ABS` -> `NK.cell.activated_CIBERSORT.ABS`
## • `Monocyte_CIBERSORT-ABS` -> `Monocyte_CIBERSORT.ABS`
## • `Macrophage M0_CIBERSORT-ABS` -> `Macrophage.M0_CIBERSORT.ABS`
## • `Macrophage M1_CIBERSORT-ABS` -> `Macrophage.M1_CIBERSORT.ABS`
## • `Macrophage M2_CIBERSORT-ABS` -> `Macrophage.M2_CIBERSORT.ABS`
## • `Myeloid dendritic cell resting_CIBERSORT-ABS` ->
## `Myeloid.dendritic.cell.resting_CIBERSORT.ABS`
## • `Myeloid dendritic cell activated_CIBERSORT-ABS` ->
## `Myeloid.dendritic.cell.activated_CIBERSORT.ABS`
## • `Mast cell activated_CIBERSORT-ABS` -> `Mast.cell.activated_CIBERSORT.ABS`
## • `Mast cell resting_CIBERSORT-ABS` -> `Mast.cell.resting_CIBERSORT.ABS`
## • `Eosinophil_CIBERSORT-ABS` -> `Eosinophil_CIBERSORT.ABS`
## • `Neutrophil_CIBERSORT-ABS` -> `Neutrophil_CIBERSORT.ABS`
## • `B cell_QUANTISEQ` -> `B.cell_QUANTISEQ`
## • `Macrophage M1_QUANTISEQ` -> `Macrophage.M1_QUANTISEQ`
## • `Macrophage M2_QUANTISEQ` -> `Macrophage.M2_QUANTISEQ`
## • `NK cell_QUANTISEQ` -> `NK.cell_QUANTISEQ`
## • `T cell CD4+ (non-regulatory)_QUANTISEQ` ->
## `T.cell.CD4...non.regulatory._QUANTISEQ`
## • `T cell CD8+_QUANTISEQ` -> `T.cell.CD8._QUANTISEQ`
## • `T cell regulatory (Tregs)_QUANTISEQ` ->
## `T.cell.regulatory..Tregs._QUANTISEQ`
## • `Myeloid dendritic cell_QUANTISEQ` -> `Myeloid.dendritic.cell_QUANTISEQ`
## • `uncharacterized cell_QUANTISEQ` -> `uncharacterized.cell_QUANTISEQ`
## • `T cell_MCPCOUNTER` -> `T.cell_MCPCOUNTER`
## • `T cell CD8+_MCPCOUNTER` -> `T.cell.CD8._MCPCOUNTER`
## • `cytotoxicity score_MCPCOUNTER` -> `cytotoxicity.score_MCPCOUNTER`
## • `NK cell_MCPCOUNTER` -> `NK.cell_MCPCOUNTER`
## • `B cell_MCPCOUNTER` -> `B.cell_MCPCOUNTER`
## • `Macrophage/Monocyte_MCPCOUNTER` -> `Macrophage.Monocyte_MCPCOUNTER`
## • `Myeloid dendritic cell_MCPCOUNTER` -> `Myeloid.dendritic.cell_MCPCOUNTER`
## • `Endothelial cell_MCPCOUNTER` -> `Endothelial.cell_MCPCOUNTER`
## • `Cancer associated fibroblast_MCPCOUNTER` ->
## `Cancer.associated.fibroblast_MCPCOUNTER`
## • `Myeloid dendritic cell activated_XCELL` ->
## `Myeloid.dendritic.cell.activated_XCELL`
## • `B cell_XCELL` -> `B.cell_XCELL`
## • `T cell CD4+ memory_XCELL` -> `T.cell.CD4..memory_XCELL`
## • `T cell CD4+ naive_XCELL` -> `T.cell.CD4..naive_XCELL`
## • `T cell CD4+ (non-regulatory)_XCELL` -> `T.cell.CD4...non.regulatory._XCELL`
## • `T cell CD4+ central memory_XCELL` -> `T.cell.CD4..central.memory_XCELL`
## • `T cell CD4+ effector memory_XCELL` -> `T.cell.CD4..effector.memory_XCELL`
## • `T cell CD8+ naive_XCELL` -> `T.cell.CD8..naive_XCELL`
## • `T cell CD8+_XCELL` -> `T.cell.CD8._XCELL`
## • `T cell CD8+ central memory_XCELL` -> `T.cell.CD8..central.memory_XCELL`
## • `T cell CD8+ effector memory_XCELL` -> `T.cell.CD8..effector.memory_XCELL`
## • `Class-switched memory B cell_XCELL` -> `Class.switched.memory.B.cell_XCELL`
## • `Common lymphoid progenitor_XCELL` -> `Common.lymphoid.progenitor_XCELL`
## • `Common myeloid progenitor_XCELL` -> `Common.myeloid.progenitor_XCELL`
## • `Myeloid dendritic cell_XCELL` -> `Myeloid.dendritic.cell_XCELL`
## • `Endothelial cell_XCELL` -> `Endothelial.cell_XCELL`
## • `Cancer associated fibroblast_XCELL` -> `Cancer.associated.fibroblast_XCELL`
## • `Granulocyte-monocyte progenitor_XCELL` ->
## `Granulocyte.monocyte.progenitor_XCELL`
## • `Hematopoietic stem cell_XCELL` -> `Hematopoietic.stem.cell_XCELL`
## • `Macrophage M1_XCELL` -> `Macrophage.M1_XCELL`
## • `Macrophage M2_XCELL` -> `Macrophage.M2_XCELL`
## • `Mast cell_XCELL` -> `Mast.cell_XCELL`
## • `B cell memory_XCELL` -> `B.cell.memory_XCELL`
## • `B cell naive_XCELL` -> `B.cell.naive_XCELL`
## • `NK cell_XCELL` -> `NK.cell_XCELL`
## • `T cell NK_XCELL` -> `T.cell.NK_XCELL`
## • `Plasmacytoid dendritic cell_XCELL` -> `Plasmacytoid.dendritic.cell_XCELL`
## • `B cell plasma_XCELL` -> `B.cell.plasma_XCELL`
## • `T cell gamma delta_XCELL` -> `T.cell.gamma.delta_XCELL`
## • `T cell CD4+ Th1_XCELL` -> `T.cell.CD4..Th1_XCELL`
## • `T cell CD4+ Th2_XCELL` -> `T.cell.CD4..Th2_XCELL`
## • `T cell regulatory (Tregs)_XCELL` -> `T.cell.regulatory..Tregs._XCELL`
## • `immune score_XCELL` -> `immune.score_XCELL`
## • `stroma score_XCELL` -> `stroma.score_XCELL`
## • `microenvironment score_XCELL` -> `microenvironment.score_XCELL`
## • `B cell_EPIC` -> `B.cell_EPIC`
## • `Cancer associated fibroblast_EPIC` -> `Cancer.associated.fibroblast_EPIC`
## • `T cell CD4+_EPIC` -> `T.cell.CD4._EPIC`
## • `T cell CD8+_EPIC` -> `T.cell.CD8._EPIC`
## • `Endothelial cell_EPIC` -> `Endothelial.cell_EPIC`
## • `NK cell_EPIC` -> `NK.cell_EPIC`
## • `uncharacterized cell_EPIC` -> `uncharacterized.cell_EPIC`
## Rows: 6475 Columns: 88
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (16): TCGA_ID, Sex, Histology, Tissue, B.cells_state_assignments, CD4.T....
## dbl (72): B.cells_S01, B.cells_S02, B.cells_S03, B.cells_S04, B.cells_S05, B...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.PCA plots
Here we analyze the PCA plots from SARIFA for their activitiy
## -- removing the lower 50% of variables based on variance
## Rows: 22584 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (6): Gene, Cytoband, (A) NON-SARIFA, (B) SARIFA, Log Ratio, Enriched in
## dbl (2): p-Value, q-Value
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Saving 8 x 6 in image
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## `geom_smooth()` using formula = 'y ~ x'